The scale of the project and the discoveries and data it generated required the dissemination of its results to be coordinated across multiple publications in peer-reviewed journals. The main results, representing one of the most important collections of scientific publications in the domain of life sciences in recent years, were published in over 30 scientific papers on September 5th 2012. The collection of articles was published jointly by four scientific journals: Nature, Genome Research, Genome Biology and BMC Genetics.

With the publication of the ENCODE package, Nature introduced a new concept in the publishing and dissemination of scientific information: the ‘threads’. The 13 online threads complement the papers by highlighting topics that are otherwise covered only in subsections of individual papers, and by providing a tool for exploring the information through a different lens. Each of them contains no original material but consists of relevant paragraphs, figures and tables from across the 30 papers, united around a specific theme, to offer to the scientific community, as a response to the increasing complexity of modern research, an enhanced and enriched way of exploring scientific publications.

Nature ENCODE explorer; an interactive guide

At the same time, to help the reader navigate through the research papers and to introduce the concept of threads to the scientific community in an intuitive, visual way, Nature created an interactive guide: the Nature ENCODE explorer, the main feature of the purpose-built website.

Nature ENCODE: the iPad app

The same concept applies to the Nature ENCODE app for the iPad, through which the user is able to access not only the full content of all the articles across the different publishers, but also other relevant information such as news, comments and videos.

Mindful of the fact that analyses of such vast amounts of data can be hard to reproduce because analyses parameters can be hard to track, Nature included virtual machines with a subset of the papers which faithfully recapitulate a given set of analyses on a given subset of data. To the best of our knowledge this was the first instance of harnessing virtual machines to safeguard transparency of data analysis and to maximize reproducibility.

Nature ENCODE team

As both transparency and reproducibility have arisen as important issues in science publishing, we intend to expand on our ENCODE experience, especially in the realm of ‘big data’ publications. Thus it is our hope that future publications of similar scope can benefit from dynamic thread generating facility, as well as sophisticated ways of ensuring transparency and reproducibility."